imod.protocols.protocol_fiducialAlignment module

class imod.protocols.protocol_fiducialAlignment.ProtImodFiducialAlignment(**kwargs)[source]

Bases: pwem.protocols.protocol.EMProtocol, tomo.protocols.protocol_base.ProtTomoBase

Construction of a fiducial model and alignment of tilt-series based on the IMOD procedure. More info:

computeFiducialAlignmentStep(tsId)[source]
computeOutputInterpolatedStackStep(tsObjId)[source]
computeOutputModelsStep(tsObjId)[source]
computeOutputStackStep(tsObjId)[source]
convertInputStep(tsObjId)[source]
createOutputFailedSet(tsObjId)[source]
createOutputStep()[source]
eraseGoldBeadsStep(tsId)[source]
generateFiducialModelStep(tsId)[source]
generateFiducialSeedStep(tsId)[source]
generateTaSolutionText(tiltAlignOutputLog, taSolutionLog, numberOfTiltImages, pixelSize)[source]

This method generates a text file containing the TA solution from the tiltalign output log.

generateTrackComStep(tsObjId)[source]
getMagnificationType()[source]
getOutputFailedSetOfTiltSeries()[source]
getOutputFiducialModelNoGaps()[source]
getOutputInterpolatedSetOfTiltSeries()[source]
getOutputSetOfCoordinates3Ds()[source]
getOutputSetOfTiltSeries()[source]
getRotationType()[source]
getSkewType()[source]
getStretchType()[source]
getSurfaceToAnalyze()[source]
getTiltAngleType()[source]
translateFiducialPointModelStep(tsObjId)[source]
translateTrackCom(ts, paramsDict)[source]
tryExceptDecorator()[source]

This decorator wraps the step in a try/except module which adds the tilt series ID to the failed TS array in case the step fails